Integrate new function on an existing NIOSII system

Hi every body,

I have developped an NIOS II application to control a Direct Digital Synthetizer through FPGA Stratix III. Now i want to integrate this new function in the old NIOS II system that control the motherboard of all the system.

I don't know where start, because in the existing NIOS II application,there is at least 30 functions..

Is there someone who can help me??

Best regards